Are there different files for the lh and rh? Sorry, never done the subfields analysis.
On 10/30/2015 01:25 PM, Bruce Fischl wrote:
Hi Heidi
I guess you could do it yourself in matlab using the aseg to figure out which hemisphere you are in
cheers Bruce
On Fri, 30 Oct 2015, Jacobs H (NP) wrote:
Hi,
Is there a way to change the index of the segmentation of the hippocampal subfields, so that when I combine left and right, FreeSurfer treats them as different regions?
Thanks! Best Heidi
I just checked again in freeview and indeed they have the same index (e.g. CA1 has value 206 for left and also for right).
On 10/27/15, 5:01 PM, "Douglas Greve" greve@nmr.mgh.harvard.edu wrote:
The color is not important. The question is whether they have a different index. Can you confirm that lh and rh have the same index?
On 10/27/15 11:53 AM, Jacobs H (NP) wrote:
Hi Doug,
Yes, for the aseg they are. But not for the hippocampal subfields: left and right have the same color coding. I am creating one segmentation, including left and right hippocampal subfields and aparc, for partial volume correction. Any idea how I can make the labels for the hippocampal subfields different (freesurfer version 6)?
Thanks Heidi
On 10/27/15, 4:32 PM, "Douglas Greve" greve@nmr.mgh.harvard.edu wrote:
> The indices should be different. Eg, 17 is left hippo, 53 is right > hippo. If you click on them in freeview and different labels > appear, > then FS knows they are different > > On 10/24/15 9:29 PM, Jacobs H (NP) wrote: >> Hi. >> >> Just one another related question: now that I was able to combine >> left >> and >> right hippocampal subfields with the aparc-aseg correctly, I >> noticed >> that >> the left and right hippocampal subfields have the same color >> labels >> and >> codes. What would be the best way to make sure that FreeSurfer >> understand >> that the left and right subfields (e.g. Left and right CA1) are >> different >> areas? >> >> Thanks! >> Heidi >> >> On 10/21/15, 11:01 PM, "Jacobs H (NP)" >> h.jacobs@maastrichtuniversity.nl >> wrote: >> >>> Thanks! Works wonderful! >>> Heidi >>> >>> On 10/21/15, 10:50 PM, "Douglas N Greve" >>> greve@nmr.mgh.harvard.edu >>> wrote: >>> >>>> If you want to remove them, you can use mri_binarize with the >>>> --replace >>>> option, replacing them with whatever you want. >>>> >>>> On 10/21/2015 04:38 PM, Jacobs H (NP) wrote: >>>>> Hi, >>>>> >>>>> I am trying to generate a segmentation file containing the >>>>> aseg+aparc >>>>> but replacing the hippocampus with the hippocampal subfields. >>>>> With mergeseg I was able to merge the segmentations, but >>>>> unfortunately >>>>> parts of the ³old² hippocampus (labeled as 17 and 53) are still >>>>> in >>>>> there (as the area covered by the subfields is not 100% >>>>> equal to >>>>> the >>>>> hippocampus of the aseg). >>>>> How can I remove the remains of the old hippocampal labels? >>>>> >>>>> Many thanks! >>>>> Best >>>>> Heidi >>>>> >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> -- >>>> Douglas N. Greve, Ph.D. >>>> MGH-NMR Center >>>> greve@nmr.mgh.harvard.edu >>>> Phone Number: 617-724-2358 >>>> Fax: 617-726-7422 >>>> >>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>> Outgoing: >>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> The information in this e-mail is intended only for the >>>> person to >>>> whom it >>>> is >>>> addressed. If you believe this e-mail was sent to you in >>>> error and >>>> the >>>> e-mail >>>> contains patient information, please contact the Partners >>>> Compliance >>>> HelpLine at >>>> http://www.partners.org/complianceline . If the e-mail was >>>> sent to >>>> you in >>>> error >>>> but does not contain patient information, please contact the >>>> sender >>>> and >>>> properly >>>> dispose of the e-mail. >>>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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